Programmable DNA Scissors Found for Bacterial Immune System

ScienceDaily (June 28, 2012) — Genetic engineers and genomics researchers should welcome the news from the Lawrence Berkeley National Laboratory (Berkeley Lab) where an international team of scientists has discovered a new and possibly more effective means of editing genomes. This discovery holds potentially big implications for advanced biofuels and therapeutic drugs, as genetically modified microorganisms, such as bacteria and fungi, are expected to play a key role in the green chemistry production of these and other valuable chemical products.

Programmable DNA scissors: A double-RNA structure in the bacterial immune system has been discovered that directs Cas9 protein to cleave and destroy invading DNA at specific nucleotide sequences. This same dual RNA structure should be programmable for genome editing. (Credit: Image by H. Adam Steinberg, artforscience.com)

Jennifer Doudna, a biochemist with Berkeley Lab's Physical Biosciences Division and professor at the University of California (UC) Berkeley, helped lead the team that identified a double-RNA structure responsible for directing a bacterial protein to cleave foreign DNA at specific nucleotide sequences. Furthermore, the research team found that it is possible to program the protein with a single RNA to enable cleavage of essentially any DNA sequence.
"We've discovered the mechanism behind the RNA-guided cleavage of double-stranded DNA that is central to the bacterial acquired immunity system," says Doudna, who holds appointments with UC Berkeley's Department of Molecular and Cell Biology and Department of Chemistry, and is an investigator with the Howard Hughes Medical Institute (HHMI). "Our results could provide genetic engineers with a new and promising alternative to artificial enzymes for gene targeting and genome editing in bacteria and other cell types."
Doudna is one of two corresponding authors of a paper in the journal Science describing this work titled "A programmable dual RNA-guided DNA endonuclease in adaptive bacterial immunity." The second corresponding author is Emmanuelle Charpentier of the Laboratory for Molecular Infection Medicine at Sweden's Umeĺ University. Other co-authors of the paper were Martin Jinek, Krzysztof Chylinski, Ines Fonfara and Michael Hauer.
Bacterial and archaeon microbes face a never-ending onslaught from viruses and invading circles of nucleic acid known as plasmids. To survive, the microbes deploy an adaptive-type nucleic acid-based immune system that revolves around a genetic element known as CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats. Through the combination of CRISPRs and associated endonucleases, called CRISPR-associated -- "Cas" -- proteins, bacteria and archaeons are able to utilize small customized crRNA molecules (for CRISPR-derived RNA) to target and destroy the DNA of invading viruses and plasmids.
There are three distinct types of CRISPR/Cas immunity systems. Doudna and her colleagues studied the Type II system which relies exclusively upon one family of endonucleases for the targeting and cleaving of foreign DNA, the Cas9 proteins.
"For the Type II CRISPR/Cas system, we found that crRNA connects via base-pairs with a trans-activating RNA (tracrRNA), to form a two-RNA structure," Doudna says. "These dual RNA molecules (tracrRNA:crRNA) direct Cas9 proteins to introduce double-stranded DNA breaks at specific sites targeted by the crRNA-guide sequence."
Doudna and her colleagues demonstrated that the dual tracrRNA:crRNA molecules can be engineered as a single RNA chimera for site-specific DNA cleavage, opening the door to RNA-programmable genome editing.
"Cas9 binds to the tracrRNA:crRNA complex which in turn directs it to a specific DNA sequence through base-pairing between the crRNA and the target DNA," Doudna says. "Microbes use this elegant mechanism to cleave and destroy viruses and plasmids, but for genome editing, the system could be used to introduce targeted DNA changes into the genome.
Doudna notes that the "beauty of CRISPR loci" is that they can be moved around on plasmids.
"It is well-established that CRISPR systems can be transplanted into heterologous bacterial strains," she says. "Also, there is evidence to suggest that CRISPR loci are horizontally transferred in nature."
Doudna and her colleagues are now in the process of gathering more details on how the RNA-guided cleavage reaction works and testing whether the system will work in eukaryotic organisms including fungi, worms, plants and human cells.
"Although we've not yet demonstrated genome editing, given the mechanism we describe it is now a very real possibility," Doudna says.
This work was funded primarily by the Howard Hughes Medical Institute, the Austrian Science Fund and the Swedish Research Council.

"Interesting" is very vague But nothing spectacular when it comes to general science AFAIK. But in specialization fields, I bet lots. The thing with science nowadays is that tons of research has been done and published, so you really need novel discoveries to be able to publish in high impact factor journals - so it's becoming harder to do so. Last year there was a Nature publication involving a nematode that was isolated from a gold mine or somewhere - deep subsurface. Quite interesting finding eukaryotes in such extreme environments

"Interesting" is very vague But nothing spectacular when it comes to general science AFAIK. But in specialization fields, I bet lots. The thing with science nowadays is that tons of research has been done and published, so you really need novel discoveries to be able to publish in high impact factor journals - so it's becoming harder to do so. Last year there was a Nature publication involving a nematode that was isolated from a gold mine or somewhere - deep subsurface. Quite interesting finding eukaryotes in such extreme environments

Yeah, universities all over are pushing that people start publishing more in high-impact journals (at least 3.25 or above) and that means research HAS to be novel. Thank goodness for open access journals such as PLoS ONE (impact factor of 4.4.) that accepts more than 70% of submitted articles.

So what are you up to that is going to get you into these high-impact journals? Sounds like you work with bacteria a lot.

Yeah, universities all over are pushing that people start publishing more in high-impact journals (at least 3.25 or above) and that means research HAS to be novel. Thank goodness for open access journals such as PLoS ONE (impact factor of 4.4.) that accepts more than 70% of submitted articles.

So what are you up to that is going to get you into these high-impact journals? Sounds like you work with bacteria a lot.

I'm working with patented things, so I can't say much, except that I'm working on vaccines/therapies as alternatives to antibiotics in the poultry industry I'm not really focusing on the high-impact journals though (although if I get worthy ideas and results, sure!), I care more about getting my degree with some good articles published for now (looks good on a CV to have a few on there!) Writing up articles is a-female-dog though. Really the worst part of science is writing up. Doing experiments, going to international conferences etc is way more enjoyable

I'm working with patented things, so I can't say much, except that I'm working on vaccines/therapies as alternatives to antibiotics in the poultry industry I'm not really focusing on the high-impact journals though (although if I get worthy ideas and results, sure!), I care more about getting my degree with some good articles published for now (looks good on a CV to have a few on there!) Writing up articles is a-female-dog though. Really the worst part of science is writing up. Doing experiments, going to international conferences etc is way more enjoyable

Yeah, writing up is definitely a schlep and sometimes you get reviewers that are real twats. It is fun to review articles though , and yeah international conferences, even some national conferences, are great to attend.

In the past year a group of synthetic proteins called CRISPR-Cas RNA-guided nucleases (RGNs) have generated great excitement in the scientific community as gene-editing tools. Exploiting a method that some bacteria use to combat viruses and other pathogens, CRISPR-Cas RGNs can cut through DNA strands at specific sites, allowing the insertion of new genetic material. However, a team of Massachusetts General Hospital (MGH) researchers has found a significant limitation to the use of CRISPR-Cas RGNs, production of unwanted DNA mutations at sites other than the desired target.